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- PDB-1qlw: The Atomic Resolution Structure of a Novel Bacterial Esterase -

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Basic information

Entry
Database: PDB / ID: 1qlw
TitleThe Atomic Resolution Structure of a Novel Bacterial Esterase
ComponentsESTERASE
KeywordsHYDROLASE(CARBOXYLIC ESTERASE) / ESTERASE / ANISOTROPIC REFINEMENT / ATOMIC RESOLUTION / ALPHA/BETA HYDROLASE
Function / homologyAlpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Carboxylesterase
Function and homology information
Biological speciesALCALIGENES SP. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.09 Å
AuthorsBourne, P.C. / Isupov, M.N. / Littlechild, J.A.
Citation
Journal: Structure / Year: 2000
Title: The Atomic Resolution Structure of a Novel Bacterial Esterase
Authors: Bourne, P.C. / Isupov, M.N. / Littlechild, J.A.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Crystallization and Preliminary X-Ray Diffraction Studies of a Novel Bacterial Esterase
Authors: Bourne, P.C. / Isupov, M.N. / Littlechild, J.A.
History
DepositionSep 17, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 10, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ESTERASE
B: ESTERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,6625
Polymers71,3742
Non-polymers2883
Water12,881715
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6500 Å2
ΔGint-30.2 kcal/mol
Surface area26750 Å2
MethodPQS
Unit cell
Length a, b, c (Å)134.730, 55.600, 110.200
Angle α, β, γ (deg.)90.00, 125.06, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.99234, -0.02182, 0.12158), (-0.01218, -0.9622, -0.27207), (0.12292, -0.27147, 0.95457)
Vector: 51.80933, 5.28295, -2.50379)
DetailsBIOLOGICAL_UNIT: DIMERIC

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Components

#1: Protein ESTERASE /


Mass: 35686.770 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: ALPHA/BETA HYDROLASE FOLD / Source: (gene. exp.) ALCALIGENES SP. (bacteria) / Production host: AGROBACTERIUM SP. (bacteria) / References: UniProt: Q7SIA5*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 715 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48.03 %
Crystal growpH: 7 / Details: PH 4.6
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: Bourne, P.C., (1999) Acta Crystallogr.,Sect.D, 55, 915.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
210 mMTris-HCl1drop
41.5-1.6 Mammonium sulfate1reservoir
3ammonium sulfate1dropsaturated

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8373
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 15, 1997 / Details: BENT MIRROR
RadiationMonochromator: HAMBURG / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8373 Å / Relative weight: 1
ReflectionResolution: 1.09→28 Å / Num. obs: 274290 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 14.5 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 14.5
Reflection shellResolution: 1.09→1.12 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.3 / % possible all: 98.2
Reflection shell
*PLUS
% possible obs: 98.2 %

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
MLPHAREphasing
DMphasing
RefinementMethod to determine structure: MIR / Resolution: 1.09→30 Å / SU B: 0.296 / SU ML: 0.015 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.025 / ESU R Free: 0.025
Details: THE C-TERMINAL RESIDUE WAS NOT SEEN IN THE DENSITY MAPS
RfactorNum. reflection% reflectionSelection details
Rfree0.158 1356 0.5 %RANDOM
Rwork0.143 ---
obs-272934 99.4 %-
Displacement parametersBiso mean: 21.4 Å2
Baniso -1Baniso -2Baniso -3
1-3.72 Å20 Å2-0.02 Å2
2---2.25 Å20 Å2
3----3.7 Å2
Refinement stepCycle: LAST / Resolution: 1.09→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4858 0 15 715 5588
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0090.02
X-RAY DIFFRACTIONp_angle_d0.0270.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0330.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.62
X-RAY DIFFRACTIONp_mcangle_it2.33
X-RAY DIFFRACTIONp_scbond_it2.32
X-RAY DIFFRACTIONp_scangle_it3.23
X-RAY DIFFRACTIONp_plane_restr0.0240.025
X-RAY DIFFRACTIONp_chiral_restr0.1140.15
X-RAY DIFFRACTIONp_singtor_nbd0.1640.3
X-RAY DIFFRACTIONp_multtor_nbd0.250.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.110.3
X-RAY DIFFRACTIONp_planar_tor5.67
X-RAY DIFFRACTIONp_staggered_tor12.715
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor38.120
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.1429 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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